Unit 3 DNA Replication and The Central Dogma

The Central Dogma

The process in which DNA is replicated, RNA is made, and proteins are made

Who discovered how new nucleotides were made?

Meselson and Stahl

Describe the experiment which found out what type of model DNA is

Scientists grew two types of bacteria in different mediums. (One heavy and one lighter). Then they allowed DNA to replicate in a tube, analyzing the weight (where they were floating in the water). The first generation was positioned in the middle, suggesting half new DNA and half parent strand. The second generation found both all new strands of DNA and a mix of parent strands and new strands. This led to the discovery that DNA is semiconservative.

Explain why the origin of replication of replication is A/T rich

A/T bonds are weaker than C/G, and carry less risk with damaging DNA

What do you call the area where replication happens? (Where the DNA is open)

Replication Bubble

What do you call the area exact area DNA is seperated?

Replication forks. There are two when DNA split to begin DNA replication

Difference between origins of replication in Prokaryotes and Eukaryotes

• Prokaryotes have one origin

• Eukaryotes have multiple origins

  • This is because their DNA is complex, and have multiple chromosomes

Purpose of Helicase

Breaks down hydrogen bonds to unwind the DNA double helix

Purpose of Topoisomerase

Relieves supercoiling

Purpose of Single-Stranded binding (SSB) proteins

Stabilize single-stranded DNA

Purpose of DNA polymerase

Catalyzes synthesis of DNA

• Requires single template strand with RNA primer

• Builds a second complementary DNA strand in 5’ to 3’ direction

Purpose of Primase

Adds 5-10 bases of RNA (primer) to initiate the synthesis of new DNA strand

Purpose of DNA polymerase III

Extends primer and synthesis the new DNA strand

What direction is DNA replicated in

5’ to 3’

DNA polymerase replicates both strands simultaneously, however, not in the same ___

Direction

Leading strand

Continuous strand. Made in same direction as fork movement

Lagging strand

Discontinuous strand, made in opposite direction as fork movement. Creates Okazaki fragments which need to be connected to each other.

Purpose of Polymerase I

Replaces primers with DNA

Purpose of DNA ligase

Connects Okazaki fragments

Lagging strand synthesis

RNA and DNA fragments that are not connected must be replaced with DNA and phosphate backbone

How does DNA polymerase replicate both strands at the same time and both towards the replication fork (But also not)

The lagging strand will loop around DNA polymerase II enzyme

What are similarities with replication in eukaryotes vs prokaryotes

• Semi conservative, semi discontinuous

• Has helicase, topoisomerase, and SSB

• DNA polymerase needs a template

• RNA primers

• 5' - 3' direction

Differences with replication in eukaryotes vs prokaryotes

• Many origins of replication

• Many DNA polymerases

• Chromosome endings fade over time

Purpose of Alpha DNA Polymerase

Primase activity

Purpose of delta DNA polymerase

Legging strand synthesis of nuclear DNA

Epsilon DNA polymerase

Leading-strand synthesis

What is the issue with the Chromosome ends in eukaryotes

When a primer is removed, there is a gap produced in the DNA. After so many rounds of replication, the DNA shrinks a lot

Telomeres

Repetitive nucleotides at ends of chromosomes that are meant to be disposable. This allows for cell division without fear of losing the actual chromosome and genetic information

Hayflick limit

The limit where DNA will no longer replicate due to absence or too short of telomeres. Replication could lead to damaging the actual chromosome

Telomerase

Can lengthen telomeres through reverse transcriptase and its own RNA template and an enzymatic protein component

When is telomerase expressed?

• Single celled organisms

• Stem cells

• Cancer

What could happen if telomerase is randomly activated again?

Development of tumors

The two parts of a gene

Regulatory sequence:

• Controls timing, location, and gene expression

Coding sequence

• Determines the amino acid sequence

Anatomy of eukaryotic gene (The control regions)

The control regions are non coding and include:

• Enhancers

  • Distal + proximal

• Promoter

• Terminator

Anatomy of eukaryotic gene (The transcribed region)

• Exon (Coding DNA)

  • Specifies amino acids

• Intron (Non-coding DNA)

What is gene expression?

Manifestation of a segment of DNA into a protein.

(mRNA acts as an intermediate to this process)

Three classes of RNA in gene expression

• mRNA (messenger RNA)

• tRNA (transfer RNA)

• rRNA (Ribosomal RNA)

What is the purpose of mRNA?

Contains genetic information for amino acid sequence of protein

What is the purpose of tRNA?

Transports amino acid to ribosome and transfers polypeptide chain during translation

What is the purpose of rRNA?

Structural component of ribosome

What is the purpose of small nuclear RNA?

Processing of pre-mRNA

What is the purpose of MicroRNA?

Inhibits translation of mRNA

What is the purpose of small interfering RNA

Triggers degradation of other RNA

What is the purpose of Piwi-interacting RNA (piRNA)?

Thought to regulate gametogenesis but unknown mostly

Gene expression in prokaryotes

It has no nucleus. So transcription and translation happens at the same time

Gene expression in eukaryotes

Translation occurs in nucleus. And then translation in the cytoplasm. mRNA happens before translation

Transcription vs Replication

• Translation includes opening only a portion of DNA for limited time

• Translation read from 3’ to 5’

How many strands of RNA can DNA make?

2, because of the double helix. One strand of DNA makes one unique copy. And the other does the same.

Three stages of transcription

1. Initiation

   1. RNA polymerase binds promoter and DNA unwinds

2. Elongation

   1. RNA polymerase makes mRNA

3. Termination

Prokaryotes initiation

Loading RNA polymerase at promoter region upstream of gene. Sigma factors help RNA polymerase bind to promoter region.

Eukaryotic initiation

They have many more promoter regions. (Focus on TATA region) Then, transcription factors (TFIID, TBP, TFIIA, TFIIB, TFIIF) load and direct RNA polymerase II at promoter.

How do eukaryotes use enhancers and activators?

Activator protein on bending DNA helps promote transcription.

How do eukaryotes use repressors and silencers?

Repressor reflects activators from binding to DNA and inhibits transcription.